Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM data

Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM data

Usage

filter_enhancers(putative_enhancers, database, type = NULL)

Arguments

putative_enhancers

epiRomics class database containing putative enhancer calls

database

epiRomics class database containing all data initially loaded

type

epiRomics reference containing database to validate putative enhancers against. Default NULL derives from genome: paste0(genome, "_custom_fantom").

Value

Variable of class epiRomics with filtered candidate enhancer regions

Examples

db <- make_example_database()
eso <- make_example_enhanceosome(db)
## filter_enhancers requires fantom annotations in database
tryCatch(
  filter_enhancers(eso, db),
  error = function(e) message(e$message)
)
#> epiRomicsS4 object
#>   Genome: hg38 
#>   Annotations: 2 ranges
#>   Meta: 8 rows
#>   Organism: org.Hs.eg.db 
#>   TxDb: TxDb.Hsapiens.UCSC.hg38.knownGene::TxDb.Hsapiens.UCSC.hg38.knownGene